RNA-seq analysis forVishal group at Longwood.
Contact Lorena Pantano (lpantano@hsph.harvard.edu) for additional details.
The most recent update of this html document occurred: Thu May 26 17:49:34 2016
The sections below provide code to reproduce the included results and plots.
2016-05-26 17:43:12 INFO::Using gene counts calculated from the Sailfish transcript counts.
Trimmed mean of M-values (TMM) normalization is described here
Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3). doi:10.1186/gb-2010-11-3-r25
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004075
out of 29229 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 7234, 25%
LFC < 0 (down) : 6763, 23%
outliers [1] : 63, 0.22%
low counts [2] : 6680, 23%
(mean count < 1)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results
NULL
Differential expression file at: uuo_model.tsv
Normalized counts matrix file at: uuo_model_log2_counts.tsv
Plot top 9 genes
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | symbol | description | day14vsnormal | day3vsnormal | day7vsnormal | absMaxLog2FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSMUSG00000029070 | 2091.3612 | 3.465458 | 0.1452649 | 551.9509 | 0 | 0 | Mxra8 | matrix-remodelling associated 8 | 3.465458 | 1.6290467 | 2.597665 | 3.465458 |
| ENSMUSG00000014599 | 1695.8187 | 3.508871 | 0.1486088 | 547.4308 | 0 | 0 | Csf1 | colony stimulating factor 1 (macrophage) | 3.508871 | 2.7557083 | 3.630187 | 3.630187 |
| ENSMUSG00000056025 | 986.3788 | 4.484630 | 0.1887504 | 529.0076 | 0 | 0 | Clca3a1 | chloride channel accessory 3A1 | 4.484630 | 3.0088526 | 3.940380 | 4.484630 |
| ENSMUSG00000002020 | 1384.6000 | 6.929634 | 0.2986806 | 524.6337 | 0 | 0 | Ltbp2 | latent transforming growth factor beta binding protein 2 | 6.929634 | 3.5683386 | 5.345282 | 6.929634 |
| ENSMUSG00000027188 | 1124.5795 | 3.048958 | 0.1369939 | 523.5912 | 0 | 0 | Pamr1 | peptidase domain containing associated with muscle regeneration 1 | 3.048958 | 1.3219187 | 2.100980 | 3.048958 |
| ENSMUSG00000052160 | 1246.4223 | 4.438108 | 0.1824232 | 496.6850 | 0 | 0 | Pld4 | phospholipase D family, member 4 | 4.438108 | 3.3770651 | 3.712660 | 4.438108 |
| ENSMUSG00000024610 | 38169.8961 | 3.867696 | 0.1547740 | 487.0193 | 0 | 0 | Cd74 | CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) | 3.867696 | 2.7307655 | 3.526930 | 3.867696 |
| ENSMUSG00000039899 | 386.9892 | 4.501820 | 0.2229482 | 485.2813 | 0 | 0 | Fgl2 | fibrinogen-like protein 2 | 4.501820 | 2.7829065 | 3.574216 | 4.501820 |
| ENSMUSG00000027962 | 8898.3531 | 6.012705 | 0.2314572 | 461.8957 | 0 | 0 | Vcam1 | vascular cell adhesion molecule 1 | 6.012705 | 5.4154007 | 6.291891 | 6.291891 |
| ENSMUSG00000073490 | 589.3769 | 4.437952 | 0.2063104 | 454.0854 | 0 | 0 | AI607873 | expressed sequence AI607873 | 4.437952 | 3.0902410 | 3.547935 | 4.437952 |
| ENSMUSG00000024164 | 72619.4358 | 6.908808 | 0.2662069 | 448.7313 | 0 | 0 | C3 | complement component 3 | 6.908808 | 7.8826994 | 7.652323 | 7.882699 |
| ENSMUSG00000041696 | 794.9974 | 2.320393 | 0.1349107 | 445.6837 | 0 | 0 | Rasl12 | RAS-like, family 12 | 2.320393 | 2.7823744 | 2.665631 | 2.782374 |
| ENSMUSG00000036905 | 3421.1210 | 4.638154 | 0.2026743 | 425.4953 | 0 | 0 | C1qb | complement component 1, q subcomponent, beta polypeptide | 4.638154 | 2.6301112 | 3.727509 | 4.638154 |
| ENSMUSG00000032000 | 1470.5987 | 3.195029 | 0.1509276 | 423.9665 | 0 | 0 | Birc3 | baculoviral IAP repeat-containing 3 | 3.195029 | 2.6438771 | 3.182327 | 3.195029 |
| ENSMUSG00000049037 | 333.8236 | 5.106393 | 0.2819995 | 422.1968 | 0 | 0 | Clec4a1 | C-type lectin domain family 4, member a1 | 5.106393 | 3.1946789 | 4.323095 | 5.106393 |
| ENSMUSG00000030772 | 1628.1774 | 1.921708 | 0.1196046 | 417.1476 | 0 | 0 | Dkk3 | dickkopf WNT signaling pathway inhibitor 3 | 1.921708 | 0.0228634 | 1.233827 | 1.921708 |
| ENSMUSG00000031875 | 1843.9338 | 3.742242 | 0.1710356 | 413.4031 | 0 | 0 | Cmtm3 | CKLF-like MARVEL transmembrane domain containing 3 | 3.742242 | 2.6701055 | 3.467449 | 3.742242 |
| ENSMUSG00000030217 | 512.6841 | 3.806288 | 0.1930331 | 409.9233 | 0 | 0 | Art4 | ADP-ribosyltransferase 4 | 3.806288 | 2.1800739 | 3.115946 | 3.806288 |
| ENSMUSG00000055653 | 6216.8719 | 3.508102 | 0.1848132 | 403.9996 | 0 | 0 | Gpc3 | glypican 3 | 3.508102 | 4.0084280 | 4.316856 | 4.316856 |
| ENSMUSG00000062980 | 715.8856 | 3.408425 | 0.1812793 | 399.8000 | 0 | 0 | Cped1 | cadherin-like and PC-esterase domain containing 1 | 3.408425 | 1.2519091 | 2.336112 | 3.408425 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0030593 | GO:0030593 | neutrophil chemotaxis | 28/684 | 81/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0070098 | GO:0070098 | chemokine-mediated signaling pathway | 20/684 | 55/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002685 | GO:0002685 | regulation of leukocyte migration | 30/684 | 155/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0006953 | GO:0006953 | acute-phase response | 17/684 | 41/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002526 | GO:0002526 | acute inflammatory response | 25/684 | 111/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0071347 | GO:0071347 | cellular response to interleukin-1 | 19/684 | 61/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0070374 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 28/684 | 166/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002274 | GO:0002274 | myeloid leukocyte activation | 27/684 | 162/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0050707 | GO:0050707 | regulation of cytokine secretion | 26/684 | 153/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0030574 | GO:0030574 | collagen catabolic process | 12/684 | 24/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0032963 | GO:0032963 | collagen metabolic process | 19/684 | 78/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0022409 | GO:0022409 | positive regulation of cell-cell adhesion | 29/684 | 201/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0034341 | GO:0034341 | response to interferon-gamma | 19/684 | 83/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0048520 | GO:0048520 | positive regulation of behavior | 24/684 | 150/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0042129 | GO:0042129 | regulation of T cell proliferation | 23/684 | 149/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002703 | GO:0002703 | regulation of leukocyte mediated immunity | 23/684 | 175/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0071216 | GO:0071216 | cellular response to biotic stimulus | 26/684 | 222/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:1903708 | GO:1903708 | positive regulation of hemopoiesis | 23/684 | 177/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0002449 | GO:0002449 | lymphocyte mediated immunity | 27/684 | 242/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0006909 | GO:0006909 | phagocytosis | 22/684 | 167/23276 | 0.0000000 | 0.0000002 | 0.0000001 |
| GO:0002573 | GO:0002573 | myeloid leukocyte differentiation | 23/684 | 185/23276 | 0.0000000 | 0.0000002 | 0.0000002 |
| GO:0030198 | GO:0030198 | extracellular matrix organization | 24/684 | 210/23276 | 0.0000000 | 0.0000005 | 0.0000004 |
| GO:0007162 | GO:0007162 | negative regulation of cell adhesion | 25/684 | 230/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0030217 | GO:0030217 | T cell differentiation | 25/684 | 230/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0019835 | GO:0019835 | cytolysis | 10/684 | 33/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0042742 | GO:0042742 | defense response to bacterium | 26/684 | 262/23276 | 0.0000001 | 0.0000021 | 0.0000015 |
| GO:0048771 | GO:0048771 | tissue remodeling | 20/684 | 163/23276 | 0.0000001 | 0.0000022 | 0.0000016 |
| GO:0045089 | GO:0045089 | positive regulation of innate immune response | 20/684 | 168/23276 | 0.0000001 | 0.0000035 | 0.0000025 |
| GO:1903035 | GO:1903035 | negative regulation of response to wounding | 19/684 | 164/23276 | 0.0000004 | 0.0000099 | 0.0000072 |
| GO:0046879 | GO:0046879 | hormone secretion | 28/684 | 324/23276 | 0.0000004 | 0.0000104 | 0.0000075 |
| GO:0007596 | GO:0007596 | blood coagulation | 19/684 | 173/23276 | 0.0000009 | 0.0000204 | 0.0000147 |
| GO:0006631 | GO:0006631 | fatty acid metabolic process | 29/684 | 359/23276 | 0.0000010 | 0.0000226 | 0.0000163 |
| GO:0031639 | GO:0031639 | plasminogen activation | 7/684 | 21/23276 | 0.0000015 | 0.0000303 | 0.0000219 |
| GO:0031589 | GO:0031589 | cell-substrate adhesion | 24/684 | 284/23276 | 0.0000040 | 0.0000751 | 0.0000542 |
| GO:0044070 | GO:0044070 | regulation of anion transport | 16/684 | 141/23276 | 0.0000041 | 0.0000771 | 0.0000556 |
| GO:0016525 | GO:0016525 | negative regulation of angiogenesis | 12/684 | 81/23276 | 0.0000042 | 0.0000772 | 0.0000557 |
| GO:0042063 | GO:0042063 | gliogenesis | 22/684 | 259/23276 | 0.0000092 | 0.0001512 | 0.0001090 |
| GO:0002478 | GO:0002478 | antigen processing and presentation of exogenous peptide antigen | 7/684 | 27/23276 | 0.0000098 | 0.0001592 | 0.0001148 |
| GO:0048871 | GO:0048871 | multicellular organismal homeostasis | 25/684 | 320/23276 | 0.0000101 | 0.0001620 | 0.0001169 |
| GO:0043491 | GO:0043491 | protein kinase B signaling | 16/684 | 154/23276 | 0.0000129 | 0.0001997 | 0.0001441 |
| GO:0019233 | GO:0019233 | sensory perception of pain | 14/684 | 127/23276 | 0.0000228 | 0.0003284 | 0.0002369 |
| GO:0010466 | GO:0010466 | negative regulation of peptidase activity | 19/684 | 220/23276 | 0.0000294 | 0.0004106 | 0.0002962 |
| GO:0050673 | GO:0050673 | epithelial cell proliferation | 26/684 | 363/23276 | 0.0000305 | 0.0004243 | 0.0003061 |
| GO:0034113 | GO:0034113 | heterotypic cell-cell adhesion | 8/684 | 43/23276 | 0.0000312 | 0.0004304 | 0.0003105 |
| GO:0034765 | GO:0034765 | regulation of ion transmembrane transport | 27/684 | 395/23276 | 0.0000485 | 0.0006341 | 0.0004574 |
| GO:0002507 | GO:0002507 | tolerance induction | 6/684 | 24/23276 | 0.0000539 | 0.0006905 | 0.0004981 |
| GO:0001503 | GO:0001503 | ossification | 26/684 | 378/23276 | 0.0000601 | 0.0007643 | 0.0005513 |
| GO:0070206 | GO:0070206 | protein trimerization | 8/684 | 48/23276 | 0.0000713 | 0.0008890 | 0.0006413 |
| GO:0016053 | GO:0016053 | organic acid biosynthetic process | 20/684 | 256/23276 | 0.0000758 | 0.0009217 | 0.0006649 |
| GO:0051797 | GO:0051797 | regulation of hair follicle development | 5/684 | 17/23276 | 0.0000996 | 0.0011708 | 0.0008446 |
| GO:0060541 | GO:0060541 | respiratory system development | 19/684 | 241/23276 | 0.0001008 | 0.0011781 | 0.0008498 |
| GO:0010876 | GO:0010876 | lipid localization | 22/684 | 305/23276 | 0.0001101 | 0.0012712 | 0.0009170 |
| GO:0001763 | GO:0001763 | morphogenesis of a branching structure | 18/684 | 229/23276 | 0.0001580 | 0.0017610 | 0.0012703 |
| GO:0072593 | GO:0072593 | reactive oxygen species metabolic process | 18/684 | 230/23276 | 0.0001669 | 0.0018488 | 0.0013336 |
| GO:1901616 | GO:1901616 | organic hydroxy compound catabolic process | 8/684 | 55/23276 | 0.0001920 | 0.0020736 | 0.0014958 |
| GO:0035458 | GO:0035458 | cellular response to interferon-beta | 6/684 | 30/23276 | 0.0002047 | 0.0021798 | 0.0015724 |
| GO:0006568 | GO:0006568 | tryptophan metabolic process | 4/684 | 11/23276 | 0.0002069 | 0.0021798 | 0.0015724 |
| GO:0042493 | GO:0042493 | response to drug | 17/684 | 215/23276 | 0.0002221 | 0.0023338 | 0.0016835 |
| GO:2000108 | GO:2000108 | positive regulation of leukocyte apoptotic process | 6/684 | 31/23276 | 0.0002476 | 0.0025332 | 0.0018273 |
| GO:0043547 | GO:0043547 | positive regulation of GTPase activity | 19/684 | 260/23276 | 0.0002687 | 0.0027416 | 0.0019777 |
| GO:0015711 | GO:0015711 | organic anion transport | 23/684 | 354/23276 | 0.0003566 | 0.0035084 | 0.0025308 |
| GO:0016051 | GO:0016051 | carbohydrate biosynthetic process | 14/684 | 164/23276 | 0.0003599 | 0.0035142 | 0.0025350 |
| GO:0008202 | GO:0008202 | steroid metabolic process | 19/684 | 268/23276 | 0.0003927 | 0.0037865 | 0.0027314 |
| GO:1990267 | GO:1990267 | response to transition metal nanoparticle | 9/684 | 78/23276 | 0.0004637 | 0.0043419 | 0.0031320 |
| GO:0006898 | GO:0006898 | receptor-mediated endocytosis | 15/684 | 189/23276 | 0.0004907 | 0.0045720 | 0.0032980 |
| GO:0035588 | GO:0035588 | G-protein coupled purinergic receptor signaling pathway | 4/684 | 15/23276 | 0.0007791 | 0.0065993 | 0.0047604 |
| GO:0042692 | GO:0042692 | muscle cell differentiation | 23/684 | 376/23276 | 0.0008177 | 0.0068893 | 0.0049697 |
| GO:0061458 | GO:0061458 | reproductive system development | 24/684 | 412/23276 | 0.0012452 | 0.0097083 | 0.0070031 |
| GO:0006968 | GO:0006968 | cellular defense response | 4/684 | 17/23276 | 0.0012963 | 0.0099859 | 0.0072034 |
| GO:0033622 | GO:0033622 | integrin activation | 4/684 | 17/23276 | 0.0012963 | 0.0099859 | 0.0072034 |
We used diana function inside cluster R package to separate genes using the expression correlation with time. Clusters with more than 15 genes are shown. A GO and KEGG enrichment is done for each group.
A summary of diana function is copied here:
The diana-algorithm constructs a hierarchy of clusterings, starting with one large cluster containing all n observations. Clusters are divided until each cluster contains only a single observation.
At each stage, the cluster with the largest diameter is selected. (The diameter of a cluster is the largest dissimilarity between any two of its observations.)
To divide the selected cluster, the algorithm first looks for its most disparate observation (i.e., which has the largest average dissimilarity to the other observations of the selected cluster). This observation initiates the "splinter group". In subsequent steps, the algorithm reassigns observations that are closer to the "splinter group" than to the "old party". The result is a division of the selected cluster into two new clusters.
Working with 855 genes
Working with 855 genes.
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu05150 | mmu05150 | NA | 17/159 | 51/6698 | 0.0000000 | 0.0000000 | 0.0000000 |
| mmu04060 | mmu04060 | NA | 28/159 | 246/6698 | 0.0000000 | 0.0000000 | 0.0000000 |
| mmu05323 | mmu05323 | NA | 14/159 | 85/6698 | 0.0000000 | 0.0000003 | 0.0000002 |
| mmu05146 | mmu05146 | NA | 16/159 | 116/6698 | 0.0000000 | 0.0000003 | 0.0000002 |
| mmu04062 | mmu04062 | NA | 20/159 | 189/6698 | 0.0000000 | 0.0000003 | 0.0000002 |
| mmu05140 | mmu05140 | NA | 12/159 | 65/6698 | 0.0000000 | 0.0000005 | 0.0000004 |
| mmu04145 | mmu04145 | NA | 19/159 | 179/6698 | 0.0000000 | 0.0000006 | 0.0000004 |
| mmu04514 | mmu04514 | NA | 15/159 | 154/6698 | 0.0000031 | 0.0000416 | 0.0000288 |
| mmu04640 | mmu04640 | NA | 11/159 | 83/6698 | 0.0000035 | 0.0000416 | 0.0000288 |
| mmu04380 | mmu04380 | NA | 13/159 | 118/6698 | 0.0000038 | 0.0000416 | 0.0000288 |
| mmu04650 | mmu04650 | NA | 13/159 | 125/6698 | 0.0000072 | 0.0000695 | 0.0000481 |
| mmu05332 | mmu05332 | NA | 9/159 | 58/6698 | 0.0000075 | 0.0000695 | 0.0000481 |
| mmu05144 | mmu05144 | NA | 8/159 | 47/6698 | 0.0000121 | 0.0001033 | 0.0000715 |
| mmu04940 | mmu04940 | NA | 9/159 | 63/6698 | 0.0000151 | 0.0001138 | 0.0000788 |
| mmu05310 | mmu05310 | NA | 6/159 | 24/6698 | 0.0000154 | 0.0001138 | 0.0000788 |
| mmu05020 | mmu05020 | NA | 6/159 | 35/6698 | 0.0001494 | 0.0010366 | 0.0007176 |
| mmu04512 | mmu04512 | NA | 9/159 | 86/6698 | 0.0001839 | 0.0012006 | 0.0008311 |
| mmu05330 | mmu05330 | NA | 7/159 | 56/6698 | 0.0003248 | 0.0020030 | 0.0013866 |
| mmu04672 | mmu04672 | NA | 6/159 | 45/6698 | 0.0006164 | 0.0034696 | 0.0024019 |
| mmu04612 | mmu04612 | NA | 8/159 | 81/6698 | 0.0006252 | 0.0034696 | 0.0024019 |
| mmu05322 | mmu05322 | NA | 11/159 | 152/6698 | 0.0009243 | 0.0048857 | 0.0033822 |
| mmu04610 | mmu04610 | NA | 7/159 | 76/6698 | 0.0020605 | 0.0103960 | 0.0071969 |
| mmu04621 | mmu04621 | NA | 6/159 | 58/6698 | 0.0023775 | 0.0114740 | 0.0079431 |
| mmu04620 | mmu04620 | NA | 8/159 | 101/6698 | 0.0026338 | 0.0116941 | 0.0080955 |
| mmu05142 | mmu05142 | NA | 8/159 | 101/6698 | 0.0026338 | 0.0116941 | 0.0080955 |
| mmu05143 | mmu05143 | NA | 4/159 | 32/6698 | 0.0065507 | 0.0279665 | 0.0193604 |
| mmu05320 | mmu05320 | NA | 6/159 | 72/6698 | 0.0069955 | 0.0287591 | 0.0199091 |
| mmu04510 | mmu04510 | NA | 11/159 | 200/6698 | 0.0078135 | 0.0309751 | 0.0214432 |
| mmu05014 | mmu05014 | NA | 5/159 | 56/6698 | 0.0102021 | 0.0370666 | 0.0256601 |
| mmu04974 | mmu04974 | NA | 6/159 | 78/6698 | 0.0102422 | 0.0370666 | 0.0256601 |
| mmu04630 | mmu04630 | NA | 9/159 | 153/6698 | 0.0103519 | 0.0370666 | 0.0256601 |
| mmu04664 | mmu04664 | NA | 6/159 | 80/6698 | 0.0115296 | 0.0399934 | 0.0276863 |
| mmu04080 | mmu04080 | NA | 13/159 | 277/6698 | 0.0141966 | 0.0477521 | 0.0330574 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0030593 | GO:0030593 | neutrophil chemotaxis | 24/400 | 81/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0097529 | GO:0097529 | myeloid leukocyte migration | 29/400 | 152/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0070098 | GO:0070098 | chemokine-mediated signaling pathway | 15/400 | 55/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0032103 | GO:0032103 | positive regulation of response to external stimulus | 29/400 | 289/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:1903037 | GO:1903037 | regulation of leukocyte cell-cell adhesion | 28/400 | 268/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002443 | GO:0002443 | leukocyte mediated immunity | 30/400 | 313/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0050727 | GO:0050727 | regulation of inflammatory response | 28/400 | 271/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002274 | GO:0002274 | myeloid leukocyte activation | 22/400 | 162/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002687 | GO:0002687 | positive regulation of leukocyte migration | 19/400 | 117/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0019221 | GO:0019221 | cytokine-mediated signaling pathway | 29/400 | 314/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0032963 | GO:0032963 | collagen metabolic process | 16/400 | 78/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:1902105 | GO:1902105 | regulation of leukocyte differentiation | 25/400 | 249/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002250 | GO:0002250 | adaptive immune response | 29/400 | 372/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0050707 | GO:0050707 | regulation of cytokine secretion | 19/400 | 153/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0002237 | GO:0002237 | response to molecule of bacterial origin | 26/400 | 316/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:0048520 | GO:0048520 | positive regulation of behavior | 17/400 | 150/23276 | 0.0000000 | 0.0000000 | 0.0000000 |
| GO:1903708 | GO:1903708 | positive regulation of hemopoiesis | 18/400 | 177/23276 | 0.0000000 | 0.0000001 | 0.0000000 |
| GO:0002253 | GO:0002253 | activation of immune response | 23/400 | 295/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0006897 | GO:0006897 | endocytosis | 30/400 | 495/23276 | 0.0000000 | 0.0000001 | 0.0000001 |
| GO:0030198 | GO:0030198 | extracellular matrix organization | 19/400 | 210/23276 | 0.0000000 | 0.0000002 | 0.0000001 |
| GO:0050708 | GO:0050708 | regulation of protein secretion | 25/400 | 391/23276 | 0.0000000 | 0.0000007 | 0.0000005 |
| GO:0042742 | GO:0042742 | defense response to bacterium | 19/400 | 262/23276 | 0.0000002 | 0.0000041 | 0.0000028 |
| GO:0048002 | GO:0048002 | antigen processing and presentation of peptide antigen | 10/400 | 67/23276 | 0.0000002 | 0.0000052 | 0.0000036 |
| GO:0042060 | GO:0042060 | wound healing | 21/400 | 326/23276 | 0.0000003 | 0.0000064 | 0.0000044 |
| GO:0032890 | GO:0032890 | regulation of organic acid transport | 9/400 | 60/23276 | 0.0000008 | 0.0000173 | 0.0000120 |
| GO:0043491 | GO:0043491 | protein kinase B signaling | 13/400 | 154/23276 | 0.0000028 | 0.0000518 | 0.0000359 |
| GO:0043547 | GO:0043547 | positive regulation of GTPase activity | 17/400 | 260/23276 | 0.0000030 | 0.0000546 | 0.0000379 |
| GO:0007229 | GO:0007229 | integrin-mediated signaling pathway | 9/400 | 76/23276 | 0.0000062 | 0.0001029 | 0.0000713 |
| GO:0051797 | GO:0051797 | regulation of hair follicle development | 5/400 | 17/23276 | 0.0000076 | 0.0001228 | 0.0000850 |
| GO:0019233 | GO:0019233 | sensory perception of pain | 11/400 | 127/23276 | 0.0000126 | 0.0001950 | 0.0001351 |
| GO:2000108 | GO:2000108 | positive regulation of leukocyte apoptotic process | 6/400 | 31/23276 | 0.0000127 | 0.0001950 | 0.0001351 |
| GO:0043588 | GO:0043588 | skin development | 16/400 | 265/23276 | 0.0000157 | 0.0002337 | 0.0001619 |
| GO:0060541 | GO:0060541 | respiratory system development | 15/400 | 241/23276 | 0.0000202 | 0.0002948 | 0.0002042 |
| GO:0060346 | GO:0060346 | bone trabecula formation | 4/400 | 11/23276 | 0.0000258 | 0.0003602 | 0.0002495 |
| GO:0001503 | GO:0001503 | ossification | 19/400 | 378/23276 | 0.0000337 | 0.0004557 | 0.0003157 |
| GO:0034765 | GO:0034765 | regulation of ion transmembrane transport | 19/400 | 395/23276 | 0.0000608 | 0.0007541 | 0.0005223 |
| GO:0033622 | GO:0033622 | integrin activation | 4/400 | 17/23276 | 0.0001713 | 0.0018024 | 0.0012484 |
| GO:0042303 | GO:0042303 | molting cycle | 9/400 | 119/23276 | 0.0002190 | 0.0022531 | 0.0015606 |
| GO:0042692 | GO:0042692 | muscle cell differentiation | 17/400 | 376/23276 | 0.0003042 | 0.0030345 | 0.0021018 |
| GO:0061458 | GO:0061458 | reproductive system development | 18/400 | 412/23276 | 0.0003086 | 0.0030694 | 0.0021260 |
| GO:0010817 | GO:0010817 | regulation of hormone levels | 19/400 | 466/23276 | 0.0004979 | 0.0045892 | 0.0031787 |
| GO:0044708 | GO:0044708 | single-organism behavior | 19/400 | 472/23276 | 0.0005811 | 0.0052669 | 0.0036481 |
| GO:0045104 | GO:0045104 | intermediate filament cytoskeleton organization | 5/400 | 41/23276 | 0.0006585 | 0.0057303 | 0.0039690 |
| GO:0016049 | GO:0016049 | cell growth | 19/400 | 483/23276 | 0.0007651 | 0.0064191 | 0.0044461 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04610 | mmu04610 | NA | 4/24 | 76/6698 | 0.0001369 | 0.0053405 | 0.0046126 |
| mmu04620 | mmu04620 | NA | 4/24 | 101/6698 | 0.0004104 | 0.0080035 | 0.0069126 |
| mmu05150 | mmu05150 | NA | 3/24 | 51/6698 | 0.0007521 | 0.0097768 | 0.0084442 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0006953 | GO:0006953 | acute-phase response | 7/85 | 41/23276 | 0.00e+00 | 0.0000002 | 0.0000002 |
| GO:0002526 | GO:0002526 | acute inflammatory response | 8/85 | 111/23276 | 0.00e+00 | 0.0000059 | 0.0000046 |
| GO:0060326 | GO:0060326 | cell chemotaxis | 8/85 | 224/23276 | 1.70e-06 | 0.0008845 | 0.0006921 |
| GO:0055072 | GO:0055072 | iron ion homeostasis | 5/85 | 69/23276 | 5.40e-06 | 0.0021638 | 0.0016930 |
| GO:0006935 | GO:0006935 | chemotaxis | 10/85 | 491/23276 | 1.21e-05 | 0.0033540 | 0.0026242 |
| GO:0070371 | GO:0070371 | ERK1 and ERK2 cascade | 7/85 | 255/23276 | 4.16e-05 | 0.0074745 | 0.0058482 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu04060 | mmu04060 | NA | 7/22 | 246/6698 | 0.0000088 | 0.0003520 | 0.0002779 |
| mmu04145 | mmu04145 | NA | 4/22 | 179/6698 | 0.0024744 | 0.0402005 | 0.0317372 |
| mmu04062 | mmu04062 | NA | 4/22 | 189/6698 | 0.0030150 | 0.0402005 | 0.0317372 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0030595 | GO:0030595 | leukocyte chemotaxis | 6/53 | 166/23276 | 0.0000021 | 0.0015717 | 0.0010672 |
| GO:0050727 | GO:0050727 | regulation of inflammatory response | 7/53 | 271/23276 | 0.0000026 | 0.0015717 | 0.0010672 |
| GO:0002526 | GO:0002526 | acute inflammatory response | 5/53 | 111/23276 | 0.0000054 | 0.0015717 | 0.0010672 |
| GO:0002292 | GO:0002292 | T cell differentiation involved in immune response | 4/53 | 53/23276 | 0.0000065 | 0.0015717 | 0.0010672 |
| GO:0007159 | GO:0007159 | leukocyte cell-cell adhesion | 8/53 | 476/23276 | 0.0000114 | 0.0020326 | 0.0013801 |
| GO:1902107 | GO:1902107 | positive regulation of leukocyte differentiation | 5/53 | 143/23276 | 0.0000185 | 0.0024975 | 0.0016957 |
| GO:0042517 | GO:0042517 | positive regulation of tyrosine phosphorylation of Stat3 protein | 3/53 | 28/23276 | 0.0000351 | 0.0032838 | 0.0022296 |
| GO:0006935 | GO:0006935 | chemotaxis | 7/53 | 491/23276 | 0.0001186 | 0.0052874 | 0.0035900 |
| GO:0010466 | GO:0010466 | negative regulation of peptidase activity | 5/53 | 220/23276 | 0.0001430 | 0.0059557 | 0.0040438 |
| GO:1903532 | GO:1903532 | positive regulation of secretion by cell | 6/53 | 389/23276 | 0.0002480 | 0.0083567 | 0.0056740 |
| GO:0006957 | GO:0006957 | complement activation, alternative pathway | 2/53 | 11/23276 | 0.0002761 | 0.0084016 | 0.0057045 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| mmu00380 | mmu00380 | NA | 6/66 | 45/6698 | 0.0000044 | 0.0003328 | 0.0002443 |
| mmu00650 | mmu00650 | NA | 5/66 | 31/6698 | 0.0000111 | 0.0003655 | 0.0002683 |
| mmu00140 | mmu00140 | NA | 6/66 | 55/6698 | 0.0000144 | 0.0003655 | 0.0002683 |
| mmu00982 | mmu00982 | NA | 6/66 | 87/6698 | 0.0001965 | 0.0037331 | 0.0027404 |
| mmu00983 | mmu00983 | NA | 5/66 | 59/6698 | 0.0002645 | 0.0040210 | 0.0029517 |
| mmu00120 | mmu00120 | NA | 3/66 | 15/6698 | 0.0003821 | 0.0048399 | 0.0035528 |
| mmu00500 | mmu00500 | NA | 4/66 | 45/6698 | 0.0009459 | 0.0091772 | 0.0067367 |
| mmu00830 | mmu00830 | NA | 5/66 | 78/6698 | 0.0009660 | 0.0091772 | 0.0067367 |
| mmu00053 | mmu00053 | NA | 3/66 | 25/6698 | 0.0018002 | 0.0146592 | 0.0107609 |
| mmu00590 | mmu00590 | NA | 5/66 | 91/6698 | 0.0019288 | 0.0146592 | 0.0107609 |
| mmu00250 | mmu00250 | NA | 3/66 | 33/6698 | 0.0040372 | 0.0278478 | 0.0204423 |
| mmu00260 | mmu00260 | NA | 3/66 | 34/6698 | 0.0043970 | 0.0278478 | 0.0204423 |
| mmu04146 | mmu04146 | NA | 4/66 | 80/6698 | 0.0077640 | 0.0440135 | 0.0323091 |
| mmu03320 | mmu03320 | NA | 4/66 | 81/6698 | 0.0081078 | 0.0440135 | 0.0323091 |
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | |
|---|---|---|---|---|---|---|---|
| GO:0006631 | GO:0006631 | fatty acid metabolic process | 15/134 | 359/23276 | 0.0000000 | 0.0000030 | 0.0000026 |
| GO:0044283 | GO:0044283 | small molecule biosynthetic process | 16/134 | 448/23276 | 0.0000000 | 0.0000041 | 0.0000035 |
| GO:0044282 | GO:0044282 | small molecule catabolic process | 12/134 | 245/23276 | 0.0000000 | 0.0000075 | 0.0000065 |
| GO:0009072 | GO:0009072 | aromatic amino acid family metabolic process | 5/134 | 25/23276 | 0.0000003 | 0.0000566 | 0.0000487 |
| GO:0043252 | GO:0043252 | sodium-independent organic anion transport | 5/134 | 28/23276 | 0.0000005 | 0.0000628 | 0.0000540 |
| GO:0008202 | GO:0008202 | steroid metabolic process | 10/134 | 268/23276 | 0.0000036 | 0.0001830 | 0.0001574 |
| GO:0015711 | GO:0015711 | organic anion transport | 11/134 | 354/23276 | 0.0000067 | 0.0003161 | 0.0002718 |
| GO:0005996 | GO:0005996 | monosaccharide metabolic process | 9/134 | 243/23276 | 0.0000119 | 0.0005032 | 0.0004327 |
| GO:0044262 | GO:0044262 | cellular carbohydrate metabolic process | 9/134 | 263/23276 | 0.0000223 | 0.0009093 | 0.0007820 |
| GO:0006639 | GO:0006639 | acylglycerol metabolic process | 6/134 | 101/23276 | 0.0000263 | 0.0010362 | 0.0008910 |
| GO:1990267 | GO:1990267 | response to transition metal nanoparticle | 5/134 | 78/23276 | 0.0000884 | 0.0028204 | 0.0024254 |
| GO:0006833 | GO:0006833 | water transport | 3/134 | 16/23276 | 0.0000989 | 0.0030711 | 0.0026410 |
| GO:1901361 | GO:1901361 | organic cyclic compound catabolic process | 9/134 | 331/23276 | 0.0001312 | 0.0039711 | 0.0034149 |
| GO:0034377 | GO:0034377 | plasma lipoprotein particle assembly | 3/134 | 21/23276 | 0.0002300 | 0.0058998 | 0.0050735 |
(useful if replicating these results)
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel methods stats graphics grDevices utils
[8] datasets base
other attached packages:
[1] hexbin_1.27.1 vsn_3.40.0
[3] DEGreport_1.5.0 quantreg_5.24
[5] SparseM_1.7 dplyr_0.4.3
[7] cluster_2.0.4 org.Mm.eg.db_3.3.0
[9] AnnotationDbi_1.34.3 clusterProfiler_3.0.2
[11] DOSE_2.10.2 gridExtra_2.2.1
[13] logging_0.7-103 tximport_1.0.2
[15] DESeq2_1.12.2 SummarizedExperiment_1.2.2
[17] Biobase_2.32.0 GenomicRanges_1.24.0
[19] GenomeInfoDb_1.8.1 IRanges_2.6.0
[21] S4Vectors_0.10.1 BiocGenerics_0.18.0
[23] pheatmap_1.0.8 CHBUtils_0.1
[25] edgeR_3.14.0 limma_3.28.5
[27] gplots_3.0.1 reshape_0.8.5
[29] ggplot2_2.1.0 myRfunctions_0.1
[31] knitr_1.13 rmarkdown_0.9.6
[33] BiocInstaller_1.22.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.50.2 RColorBrewer_1.1-2
[4] tools_3.3.0 affyio_1.42.0 R6_2.1.2
[7] rpart_4.1-10 KernSmooth_2.23-15 Hmisc_3.17-4
[10] DBI_0.4-1 colorspace_1.2-6 nnet_7.3-12
[13] preprocessCore_1.34.0 Nozzle.R1_1.1-1 chron_2.3-47
[16] graph_1.50.0 formatR_1.4 topGO_2.24.0
[19] caTools_1.17.1 scales_0.4.0 affy_1.50.0
[22] genefilter_1.54.2 stringr_1.0.0 digest_0.6.9
[25] foreign_0.8-66 XVector_0.12.0 htmltools_0.3.5
[28] RSQLite_1.0.0 BiocParallel_1.6.2 gtools_3.5.0
[31] acepack_1.3-3.3 GOSemSim_1.30.2 magrittr_1.5
[34] GO.db_3.3.0 Formula_1.2-1 Matrix_1.2-6
[37] Rcpp_0.12.5 munsell_0.4.3 stringi_1.0-1
[40] yaml_2.1.13 zlibbioc_1.18.0 plyr_1.8.3
[43] qvalue_2.4.2 grid_3.3.0 gdata_2.17.0
[46] DO.db_2.9 lattice_0.20-33 splines_3.3.0
[49] annotate_1.50.0 locfit_1.5-9.1 igraph_1.0.1
[52] geneplotter_1.50.0 reshape2_1.4.1 XML_3.98-1.4
[55] evaluate_0.9 latticeExtra_0.6-28 data.table_1.9.6
[58] MatrixModels_0.4-1 gtable_0.2.0 tidyr_0.4.1
[61] assertthat_0.1 xtable_1.8-2 coda_0.18-1
[64] survival_2.39-4 GSEABase_1.34.0